tbuckley/cabot-search huggingface dataset:
Table of Contents
Authors: G Curigliano, K Dunton, M Rosenlund, M Janek, J Cathcart, Y Liu, P Fasching, H Iwata, M Rakaee, S Andersen, K Giannikou, E.-E Paulsen, T Kilvaer, L.-T Busund, T Berg, E Richardsen, A Lombardi, E Adib, M Pedersen, M Tafavvoghi, S Wahl, R Petersen, A Bondgaard, C Yde, C Baudet, P Licht, M Lund-Iversen, B Grønberg, L Fjellbirkeland, Å Helland, M Pøhl, D Kwiatkowski, D Boiarsky, C Lydon, E Chambers, L Sholl, M Nishino, F Skoulidis, J Heymach, J Luo, M Awad, P Janne, E Van Allen, D Barbie, N Vokes
Journal: Annals of Oncology (2023)
Protein glycosylation and glycoinformatics for novel biomarker discovery in neurodegenerative diseases
Authors: Júlia Costa, Catherine Hayes, Frédérique Lisacek
Journal: Ageing Research Reviews (2023)

Glycosylation is a common post-translational modification of brain proteins including cell surface adhesion molecules, synaptic proteins, receptors and channels, as well as intracellular proteins, with implications in brain development and functions. Using advanced state-of-the-art glycomics and glycoproteomics technologies in conjunction with glycoinformatics resources, characteristic glycosylation profiles in brain tissues are increasingly reported in the literature and growing evidence shows deregulation of glycosylation in central nervous system disorders, including aging associated neurodegenerative diseases. Glycan signatures characteristic of brain tissue are also frequently described in cerebrospinal fluid due to its enrichment in brain-derived molecules. A detailed structural analysis of brain and cerebrospinal fluid glycans collected in publications in healthy and neurodegenerative conditions was undertaken and data was compiled to create a browsable dedicated set in the GlyConnect database of glycoproteins (https://glyconnect.expasy.org/brain). The shared molecular composition of cerebrospinal fluid with brain enhances the likelihood of novel glycobiomarker discovery for neurodegeneration, which may aid in unveiling disease mechanisms, therefore, providing with novel therapeutic targets as well as diagnostic and progression monitoring tools.
Lung Cancer in the Republic of Ireland
Authors: Rachel J. Keogh, Martin P. Barr, Anna Keogh, David McMahon, Anne-Marie Baird, Seamus Cotter, David Breen, Gerard J. Fitzmaurice, David Fitzpatrick, Cathal O’Brien, Stephen P. Finn, Jarushka Naidoo
Journal: Journal of Thoracic Oncology (2023)
Strengthening the HIV prevention cascade to maximise epidemiological impact in eastern Zimbabwe: a modelling study
Authors: Michael Pickles, Simon Gregson, Louisa Moorhouse, Tawanda Dadirai, Freedom Dzamatira, Phyllis Mandizvidza, Rufurwokuda Maswera, Tafadzwa Museka, Robin Schaefer, Morten Skovdal, Ranjeeta Thomas, Blessing Tsenesa, Owen Mugurungi, Constance Nyamukapa, Timothy B Hallett
Journal: The Lancet Global Health (2023)

HIV prevention cascades provide a systematic understanding of barriers to prevention. In this study we used mathematical modelling to understand the consequences of these barriers and how the cascade could be strengthened to maximise epidemiological impact, providing potentially important insights for programmes.
Integrating global HIV services with primary health care: a key step in sustainable HIV epidemic control
Authors: Deborah Goldstein, Michael Salvatore, Robert Ferris, Benjamin Ryan Phelps, Thomas Minior
Journal: The Lancet Global Health (2023)

Ending the HIV epidemic relies in part on integrating stand-alone HIV programming with primary health-care platforms to improve population-level health and ensure sustainability. Integration of HIV and primary health care services in sub-Saharan Africa improves both outcomes. Existing models support both integrating primary health care services into existing HIV services, and incorporating HIV services into primary health care platforms, with optimal programming based on local contexts and local epidemic factors. Person-centred differentiated service delivery, community-based interventions, and a well supported health workforce form the backbone of successful integration. Strategic financing to optimise HIV and primary health care integration requires well-coordinated partnerships with host governments, private sector companies, multilateral stakeholders, development banks, and non-government organisations. Programme success will require increased flexibility of international donors' implementation guidance as well as involvement of local communities and civil society organisations. As we seek to end the HIV epidemic by 2030 amidst a constrained global economic climate, integration of HIV programming with primary health care offers an avenue of opportunity and hope.
How the EAT–Lancet Commission on food in the Anthropocene influenced discourse and research on food systems: a systematic review covering the first 2 years post-publication
Authors: Ayesha I T Tulloch, Fiona Borthwick, Diana Bogueva, Mahmoud Eltholth, Amanda Grech, Dylan Edgar, Sinead Boylan, Geraldine McNeill
Journal: The Lancet Global Health (2023)

In 2019, the EAT-Lancet Commission's report on food in the Anthropocene presented a planetary heath diet to improve health while reducing the environmental effect of food systems globally. We assessed EAT-Lancet's immediate influence on academic research and debate by conducting a systematic review of articles citing the Commission and others published from January, 2019, to April, 2021. The Commission influenced methods, results, or discourse for 192 (7·5%) of 2560 citing articles, stimulating cross-disciplinary research and debate across life sciences (47%), health and medical sciences (42%), and social sciences (11%). Sentiment analysis of 76 critiquing articles indicated that opinions were, on average, more positive than negative. Positive sentiments centred on benefits for informing policy, public health, and raising public awareness. Negative sentiments included insufficient attention to socioeconomic dimensions, feasibility, and environmental effects other than emissions. Empirical articles predominantly evaluated the effects of changed diets or food production on the environment and wellbeing (29%), compared current diets with EAT-Lancet recommendations (12%), or informed future policy and research agendas (20%). Despite limitations in EAT-Lancet's method, scope, and implementation feasibility, the academic community supported these recommendations. A broad suite of research needs was identified focusing on the effects of food processing, socioeconomic and political drivers of diet and health, and optimising consumption or production for environment and health.
Repurposing an integrated national influenza platform for genomic surveillance of SARS-CoV-2 in Ghana: a molecular epidemiological analysis
Authors: Ivy Asantewaa Asante, Sharon Nienyun Hsu, Linda Boatemaa, Lorreta Kwasah, Mildred Adusei-Poku, John Kofi Odoom, Yaw Awuku-Larbi, Benjamin H Foulkes, Joseph Oliver-Commey, Ernest Konadu Asiedu, Matthew D Parker, Oriol Mitja, Rosalind M Eggo, Leonardo de Oliveira-Martins, Franklin Asiedu-Bekoe, Dennis Odai Laryea, Patrick Kuma-Aboagye, Michael Marks, Thushan I de Silva, William Kwabena Ampofo
Journal: The Lancet Global Health (2023)

Genomic surveillance of SARS-CoV-2 is crucial for monitoring the spread of COVID-19 and guiding public health decisions, but the capacity for SARS-CoV-2 testing and sequencing in Africa is low. We integrated SARS-CoV-2 surveillance into an existing influenza surveillance network with the aim of providing insights into SARS-CoV-2 transmission and genomics in Ghana.
Pulmonary Artery Pseudoaneurysm as a Complication of Transbronchial Lung Cryobiopsy
Authors: Hiroki Ohta, Hideaki Yamakawa, Tamiko Takemura, Hidekazu Matsushima
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

"Pulmonary Artery Pseudoaneurysm as a Complication of Transbronchial Lung Cryobiopsy." American Journal of Respiratory and Critical Care Medicine, 208(4), pp. e27–e28
Green Pleural Effusion Secondary to Eosinophilic Autofluorescence
Authors: Adam Austin, Evan Asher, Jacquelyn A. Knapik, Cesar Trillo-Alvarez, Hiren J. Mehta
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

"Green Pleural Effusion Secondary to Eosinophilic Autofluorescence ." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
Curiosity and Uncertainty Resolution: Inflating the Perceived Utility of Genetic Information
Authors: Rémy Furrer, Dorit Barlevy, Stacey Pereira, Gabriel Lázaro-Muñoz
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image size Additional informationFundingThis work was supported in part by the National Institutes of Health (R01 HG011711 to GL-M).
Metformin for Treatment of Acute COVID-19: Systematic Review of Clinical Trial Data Against SARS-CoV-2
Authors: Spencer M. Erickson, Sarah L. Fenno, Nir Barzilai, George Kuchel, Jenna M. Bartley, Jamie Nicole Justice, John B. Buse, Carolyn T. Bramante
Journal: Diabetes Care (2023)

Observational and preclinical data suggest metformin may prevent severe coronavirus disease 2019 (COVID-19) outcomes.
Imperfect Methods for Imperfect Democracies: Increasing Public Participation in Gene Editing Debates
Authors: Benjamin Gregg
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article refers to:The Promise and Reality of Public Engagement in the Governance of Human Genome Editing Research Additional informationFundingThe author(s) reported there is no funding associated with the work featured in this article.
Whose Genome? Which Genetics?
Authors: Bryan Cwik
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article refers to:Rare Disease, Advocacy and Justice: Intersecting Disparities in Research and Clinical CareThe Promise and Reality of Public Engagement in the Governance of Human Genome Editing ResearchIs It Just for a Screening Program to Give People All the Information They Want?Bounded Justice, Inclusion, and the Hyper/Invisibility of Race in Precision MedicinePromoting Equality in the Governance of Heritable Human Genome Editing through Ubuntu: Reflecting on a South African Public Engagement Study DISCLOSURE STATEMENTThe author is a member of the external advisory board for the Oregon Health and Science University Center for Embryonic Cell and Gene Therapy. The author is a pro bono member and does not receive an honorarium for their service.Additional informationFundingThe author(s) reported there is no funding associated with the work featured in this article.
What Difference Can Public Engagement in Genome Editing Make, and for Whom?
Authors: Richard Milne, Ugbaad Aidid, Jerome Atutornu, Tuba Bircan, Daniela Boraschi, Alessia Costa, Sasha Henriques, Christine Patch, Anna Middleton
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article refers to:The Promise and Reality of Public Engagement in the Governance of Human Genome Editing Research Additional informationFundingThis work was supported by Wellcome Trust.
Comment on Lundeen et al. Trends in the Prevalence and Treatment of Diabetic Macular Edema and Vision-Threatening Diabetic Retinopathy Among Commercially Insured Adults Aged &amp;lt;65 Years. Diabetes Care 2023;46:687–696
Authors: Sylvie Feldman-Billard, Pascale Massin, Catherine Creuzot-Garcher
Journal: Diabetes Care (2023)
Translational Justice in Human Gene Editing: Bringing End User Engagement and Policy Together
Authors: Megan A. Allyse, Karen M. Meagher, Marsha Michie, Rosario Isasi, Kelly E. Ormond, Natasha Bonhomme, Yvonne Bombard, Heidi Howard, Kiran Musunuru, Kirsten A. Riggan, Sabina Rubeck
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article refers to:The Promise and Reality of Public Engagement in the Governance of Human Genome Editing Research Additional informationFundingThis study was funded by National Human Genome Research Institute (No. R01 HG011461).
The Australian Citizens’ Jury and Global Citizens’ Assembly on Genome Editing
Authors: Dianne Nicol, John Stanley Dryzek, Simon Niemeyer, Nicole Curato, Rebecca Paxton
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article refers to:The Promise and Reality of Public Engagement in the Governance of Human Genome Editing Research Additional informationFundingThis work was supported by Australian Research Council; Medical Research Futures Fund Genomics Health Futures Mission.
Rare Disease, Advocacy, and Caregiver Burnout
Authors: Gretchen Agans
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article refers to:Rare Disease, Advocacy and Justice: Intersecting Disparities in Research and Clinical Care Additional informationFundingThe author(s) reported there is no funding associated with the work featured in this article.
Public Engagement in Shaping Bioethics Policy: Reasons for Skepticism
Authors: Rosamond Rhodes, Gary Ostertag
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article refers to:The Promise and Reality of Public Engagement in the Governance of Human Genome Editing Research Additional informationFundingThe author(s) reported there is no funding associated with the work featured in this article.
Disclosing Reproductive Genetic Carrier Status: What about the Donor?
Authors: Dorian Accoe
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article refers to:Is It Just for a Screening Program to Give People All the Information They Want? Additional informationFundingThe author(s) reported there is no funding associated with the work featured in this article.
Effectiveness of a cardiovascular health EHR application for cancer survivors in community oncology practice: Results from WF-1804CD.
Authors: Kathryn E. Weaver, Emily Van Meter Dressler, Heidi D. Klepin, Simon Craddock Lee, Sydney Smith, Brian J Wells, W. Gregory Hundley, Glenn Jay Lesser, Chandylen L Nightingale, Alyssa Throckmorton, Marcia Hernandez, Jenny Marie Hanna, Ian T. Lackey, Kevin Heard, Randi E Foraker
Journal: Journal of Clinical Oncology (2023)

LBA12007 Background: Practice guidelines recommend cardiovascular risk assessment and counseling for cancer survivors. The Automated Heart-Health Assessment study (AH-HA: WF-1804CD, NCT# 03935282) evaluated a novel electronic health record (EHR) clinical decision support tool based on American Heart Association Simple 7 cardiovascular health (CVH) factors to promote provider-patient CVH discussions in outpatient oncology. Methods: This clinic-randomized trial (R01CA226078), coordinated by the Wake Forest NCORP Research Base (UG1CA189824), randomized NCORP oncology practices using the Epic EHR to the AH-HA tool or usual care and enrolled survivors receiving routine care at least 6 months post-curative cancer treatment. The tool rendered an interactive display of risk factors, automatically populated from the EHR, alongside a tab indicating receipt of cancer treatments with cardiotoxic potential. Survivors at AH-HA sites had tool access during a routine visit; survivors at usual care sites did not. Immediately post-visit, each survivor was asked about counseling on 7 CVH factors [body mass index, physical activity, diet, smoking status, blood pressure, cholesterol, and glucose]. The primary endpoint is survivor-reported discussion of non-ideal or missing CVH factors; with 8 randomized practices (ICC=0.03), the study design had 82% power to detect a difference of 20% reported discussions in usual care versus 40% in AH-HA. Additional clinical endpoints were documentation of CVH discussions, referrals to primary care and cardiology, and change in CVH factors over 12 months (ongoing). A mixed effects logistic regression model assessed the effect of AH-HA on CVH discussions between the arms, with study arm as a fixed effect and practice as a random effect. Results: 5 usual care and 4 AH-HA practices enrolled 645 survivors from 10/1/2020- 2/28/2023. The majority had breast cancer (82%; 8% endometrial, 5% colorectal, 5% prostate, lymphoma or multiple types). Most survivors were female (96%; 84% White/non-Hispanic, 8% Black; 3% Hispanic; mean age= 62 yrs and median time since diagnosis=3.6 yrs). 18 participants (3%) did not complete necessary assessments, leaving 627 evaluable. 87% of providers (n=15) rated the tool utility and ease of use positively. Conclusions: The AH-HA tool was acceptable and effective at promoting CVH discussions during routine follow-up care for survivors and referrals to primary care. Clinical trial information: NCT03935282 . [Table: see text]
Hunting for Progressive NAFLD in Type 2 Diabetes: Do Not Trust Liver Enzymes!
Authors: Egeria Scoditti, Giulio Marchesini, Amalia Gastaldelli
Journal: Diabetes Care (2023)

Age = 52-66 years BMI = 28-36 kg/m 2 HbA1c = 6.8-8.4% ALT = 34-70 IU/L 37% 63% High prevalence of NASH and advanced fibrosis
Reconfiguring Health: The Importance of Recognizing Embodied Subjectivity and Social Dynamics in Health
Authors: Gesine Sturm, Yann Zoldan
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article refers to:Bounded Justice, Inclusion, and the Hyper/Invisibility of Race in Precision Medicine Additional informationFundingThe author(s) reported there is no funding associated with the work featured in this article.
Ethical Considerations in Clinical Trials for Rare Genetic Diseases: The Case of Huntington’s Disease
Authors: Adys Mendizabal, Nora L. Jones
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article refers to:Rare Disease, Advocacy and Justice: Intersecting Disparities in Research and Clinical Care Additional informationFundingThe author(s) reported there is no funding associated with the work featured in this article.
End-of-Life Systemic Oncologic Treatment in the Immunotherapy Era: The Role of Race, Insurance, and Practice Setting
Authors: Maureen Canavan, Xiaoliang Wang, Mustafa Ascha, Rebecca Miksad, Timothy N. Showalter, Gregory Calip, Cary P. Gross, Kerin Adelson
Journal: Journal of Clinical Oncology (2023)

PURPOSE Receipt of antineoplastic systemic treatment near end of life (EOL) has been shown to harm patient and caregiver experience, increase hospitalizations, intensive care unit and emergency department use, and drive-up costs; yet, these rates have not declined. To understand factors contributing to use of antineoplastic EOL systemic treatment, we explored its association with practice- and patient-level factors. METHODS We included patients from a real-world electronic health record–derived deidentified database who received systemic therapy for advanced or metastatic cancer diagnosed starting in 2011 and died within 4 years between 2015 and 2019. We assessed use of EOL systemic treatment at 30 and 14 days before death. We divided treatments into three subcategories: chemotherapy alone, chemotherapy and immunotherapy in combination, and immunotherapy (with/without targeted therapy), and estimated conditional odds ratios (ORs) and 95% CIs for patient and practice factors using multivariable mixed-level logistic regression. RESULTS Among 57,791 patients from 150 practices, 19,837 received systemic treatment within 30 days of death. We observed 36.6% of White patients, 32.7% of Black patients, 43.3% of commercially insured patients, and 37.0% of Medicaid patients received EOL systemic treatment. White patients and those with commercial insurance were more likely to receive EOL systemic treatment than Black patients or those with Medicaid. Treatment at community practices was associated with higher odds of receiving 30-day systemic EOL treatment than treatment at academic centers (adjusted OR, 1.51). We observed large variations in EOL systemic treatment rates across practices. CONCLUSION In a large real-world population, EOL systemic treatment rates were related to patient race, insurance type, and practice setting. Future work should examine factors that contribute to this usage pattern and its impact on downstream care. [Media: see text]
Ethical, Legal, and Social Implications of Genomics Research: Implications for Building a More Racially Diverse Bioethics Workforce
Authors: Faith E. Fletcher
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article is referred to by:Innovating for a Just and Equitable Future in Genomic and Precision Medicine ResearchThis article refers to:Bounded Justice, Inclusion, and the Hyper/Invisibility of Race in Precision Medicine ACKNOWLEDGMENTThe author would like to thank Clarice Jacobson, Alice Story, and Sophie Schott for engaging in a brainstorming session around bioethics training programs for minority trainees.No potential conflict of interest was reported by the author(s).DISCLOSURE STATEMENTAdditional informationFundingThis work was supported in part by the National Human Genome Research Institute of the National Institutes of Health under award number K01HG011495-01.
Addressing the Burdens That Newborn Screening Imposes on Underserved Communities
Authors: Meghan E. Strenk, Courtney Berrios, Jeremy R. Garrett
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article refers to:Rare Disease, Advocacy and Justice: Intersecting Disparities in Research and Clinical Care ACKNOWLEDGMENTCourtney Berrios and Jeremy Garrett contributed equally as senior authors on the manuscript, and we wish to acknowledge them as co-senior authors.Additional informationFundingCourtney Berrios' work on this commentary was supported by a CTSA grant from National Center for Advancing Translational Sciences awarded to the Frontiers Clinical and Translational Science Institute at the University of Kansas [# UL1TR002366]. The contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH or NCATS.
Innovating for a Just and Equitable Future in Genomic and Precision Medicine Research
Authors: Deanne Dunbar Dolan, Mildred K. Cho, Sandra Soo-Jin Lee
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article refers to:Rare Disease, Advocacy and Justice: Intersecting Disparities in Research and Clinical CareThe Promise and Reality of Public Engagement in the Governance of Human Genome Editing ResearchIs It Just for a Screening Program to Give People All the Information They Want?Bounded Justice, Inclusion, and the Hyper/Invisibility of Race in Precision MedicineEthical, Legal, and Social Implications of Genomics Research: Implications for Building a More Racially Diverse Bioethics WorkforceThe Other Side of the Self-Advocacy Coin: How For-Profit Companies Can Divert the Path to Justice in Rare DiseasePromoting Equality in the Governance of Heritable Human Genome Editing through Ubuntu: Reflecting on a South African Public Engagement StudyNarrative Equity in Genomic Screening at the Population LevelCritiquing the Critique of Advocacy ACKNOWLEDGEMENTSThis special issue would not be possible without the support of the National Human Genome Research Institute and its support of the biennial ELSI Congress (Grant number U13HG010830) and the Center for ELSI Resources and Analysis (Grant number U24 HG010733). We are grateful to Editor-in-Chief, David Magnus, Executive Managing Editor Bela Fishbeyn, and the publishers of the American Journal of Bioethics, Rachel H. Lee, and several anonymous reviewers for the opportunity to present this research to the community. We hope the conclusions presented in this issue will stimulate both scholarship and action.DISCLOSURE STATEMENTThe authors declare financial support from the National Human Genome Research Institute.Additional informationFundingThis work was supported by the National Human Genome Research Institute under Grant number [U13HG010830] and Grant number [U24 HG010733].